Since the flagging and closing changes back in June, I get the impression that the flag indicator is now cached (or more properly speaking buffered). I've observed several times on both FR and CS that I visit a page, which shows no flag indicator, then I visit some other page, which shows an hours-old flag.
When I dismiss a flag and immediately reload the front page, the flag indicator does go away, so it seems that the caching is only in one direction, or maybe there's an additional check to avoid displaying 0.
As a moderator, I sometimes load a page while I'm doing other things with my computer, just to check if there are any flags. For this I really need to have up-to-date flag information.
Please do not cache the flag indicator (at least outside SO, where the difference between 400 pending flags and 450 pending flags isn't so important), or at least, do not buffer the transition from 0 to nonzero. If there's a flag, make sure that the next page load by a moderator shows that there is a flag.
Note that this is a months-old bug, that the new top bar did not cause but did not fix either.